Biochem Exam 2

Alanine

Ala, A, Non-polar

Valine

Val, V, Non-polar

Phenylalanine

Phe, F, Non-polar

Tryptophan

Trp, W, Non-polar

Leucine

Leu, L, Non-polar

Isoleucine

Ile, I, Non-polar

Methionine

Met, M, Non-polar

Proline

Pro, P, Non-polar

Serine

Ser, S, Polar

Threonine

Thr, T, Polar

Tyrosine

Tyr, Y, Polar

Asparagine

Asn, N, Polar

Glutamine

Gln, Q, Polar

Cysteine

Cys, C, Polar (creates disulfide bonds with other cysteines

Histidine

His, H, Polar (can be charged)

Lysine

Lys, K, Basic (pos charge)

Arginine

Arg, R, Basic (pos charge)

Aspartate (aspartic acid)

Asp, D, Acidic (neg charge)

Glutamate (glutamic acid)

Glu, E, Acidic (neg charge)

Glycine

Gly, G, Not charged

Rank the following according to their strength as acids--rank from strongest (1) to weakest (5).

A - 4
B - 3
C - 5
D - 2
E - 1

Which of the following would NOT form a suitable buffer?

Hydrochloric acid/chloride

Under what conditions would a carboxyl group (COOH, pK 3.5) be mostly protonated?

pH < pK

Under what conditions would a carboxyl group (COOH, pK 3.5) be mostly deprotonated?

pH > pK

In aqueous solution, globules of up to several thousand amphiphilic molecules arranged with the hydrophilic groups on the surface and the hydrophobic groups buried in the center are called _____.

micelles

What term is used to describe the exclusion of nonpolar substances from an aqueous solution?

hydrophobic effect

Which of the following is an example of the hydrophobic effect?

all are examples of the hydrophobic effect

A molecule that has both a polar and nonpolar region is called _____________.

amphiphilic

If the pK value for acetic acid (CH3COOH) is 4.76 at what pH would one observe equal amounts of CH3COO- and CH3COOH?

4.76

During metabolic acidosis, ______ ventilation excretes acid in the form of _____ .

increased; CO2

The LOWER the pK value of an acid the STRONGER the acid.

True

Which of the following bond forces are important in tertiary structure:

Hydrophobic effect
Hydrogen bonds
Disulfide bonds

Which of the following amino acid substitutions would be most likely to effect protein function?

B

Select all the commonalities between alpha helices and b-pleated sheets. (i.e. select what is similar in both types of secondary structure)

prolines and glycines aren't suitable for the secondary structure
hydrogen bonds between main chain CO and NH groups
peptide bond is planar

The formation of a dipeptide from two amino acids involves

A) side-chain complementarity.

B) loss of water.

C) oxidation of the alpha-carbon.

D) reduction of the alpha-carbon.

E) base catalysis.

B

The protein shown above is the human coronavirus protease. The structure contains 2 subunits, that have identical sequences. This protein can be classified as:

quaternary:homodimer

At what pH would an amino acid bear both a COOH and an NH2 group?

Never

All secondary structures in proteins involve helical forms.

False

Cys-Ala-Gly-Arg-Gln-Met

In the above peptide, the amino-terminal amino acid is
____ and the carboxyl-terminal amino acid is ____

Cys; Met

For the amino acid structures shown above, the protonation state of structure A is shown at ______ pH, and the protonation state of structure B is shown at _______ pH.

low; high

Choose the amino acid that would be more likely to appear on the solvent-exposed (water facing) surface of a protein.


Leu or Lys
Ser or Ala
Phe or Tyr
Trp or Gln
Asn or Ile

Lys

Ser

Tyr

Gln

Asn

Primary

The order in which the amino acids in a protein are linked by peptide bonds

Secondary

The arrangement of the backbone atoms in a polypeptide chain

Tertiary

The arrangement of all the atoms in a protein (interactions between the R groups, hydrophobic ones inside of the protein)

Quaternary

the interaction of several polypeptide chains in a multisubunit protein

Examine the four amino acids given below:

Indicate which of these amino acids are associated with the following properties:

branched aliphatic sidechain - C
basic sidechain - D
aromatic R group - B
cyclic (nonaromatic) R group - A

Which of the following amino acids carry a net positive charge at pH 7.0?

Arg, Lys

What is the net charge on the following peptide at pH 9.5?

Lys-Ala-Glu-Gln-Cys-Ile

-2

What is the net charge of the pentapeptide Ala-Cys-Ser-Glu-Asn at pH 7?

-1

Any peptide which contains 2 sulfur-containing amino acids can form an internal disulfide bond.

False

The interactions that stabilize multisubunit complexes are different than those that stabilize tertiary structure.

False

Myoglobin is _____; hemoglobin is _____.

monomeric; tetrameric

The individual hemoglobin subunits and myoglobin share similar primary structure but have rather different secondary structure.

False

Which of the following fibers is correctly paired with the protein that forms the fiber?

extracellular support fibers: collagen
microtubules: tubulin
microfilaments: actin
intermediate filaments: keratin
(all are true)

Which amino acid is critical for crosslinking of keratin fibers?

Cys (disulfide bonds)

The idea that binding of one molecule of oxygen to hemoglobin enhances further binding of oxygen to hemoglobin is called _____.

cooperativity

What is the most prevalent secondary structure observed in the proteins of intermediate filaments?

alpha helices

Which of the following statements about actin are true?

Monomeric G-actin polymerizes to form F-actin.
Actin filaments are polar (the ends can be distinguished).

Several oxygen dissociation curves are shown in the figure below. Assuming that curve 3 corresponds to isolated hemoglobin placed in a solution containing physiologic concentrations of CO2 and BPG at a pH of 7.0, indicate which of the curves reflects the following changes in conditions:

Increased BPG concentration
4

Increased pH
2

Dissociation of hemoglobin into subunits.
1

Match the feature of hemoglobin with the proper structural level.

Amino acid sequence in each of the alpha and beta polypeptide chains.
Primary Structure

8 alpha helices in each of the subunits.
Secondary Structure

Spatial relationship between every atom in the individual subunits.
Tertiary Structure

Spatial relationship between the four polypeptide chains.
Quaternary Structure

The presence of 2,3-BPG causes hemoglobin's affinity for oxygen to______.

decrease

Which amino acid is involved in heme coordination in both hemoglobin and myoglobin and is highly conserved?

Histidine

Calculate the fractional saturation for myoglobin when pO2 is a. 20 torr and b. 80 torr. Assume K=2.8.

a. 0.88
b. 0.97

Both myoglobin and hemoglobin exhibit cooperative binding to oxygen.

False

Conservative amino acid mutations (i.e. Val to Leu) are likely to affect stability or function of a protein.

False

Which of the following fatty acids have the lowest melting point?

Linoleate (18:2)

Which of the following types of lipids can be found in cell membranes?

glycerophospholipids
cholesterol
cerebrosides
gangliosides

Select the statements the describe fatty acids:

can either be saturated or unsaturated.
mostly found with an even number of carbons

In what way(s) do sphingolipids differ from glycerophospholipids?

Sphingolipids are not built on a glycerol backbone.
Sphingolipids contain an acyl group attached via an amide bond on the serine potion of the sphingosine.

Show which are characteristics of peripheral membrane proteins and which are characteristics of integral membrane proteins.

peripheral
bind to the surface of membranes

integral
have transmembrane domains

Which of the following is most likely to be an unnatural fatty acid?

17:3△t9,12,15 (uneven number of carbons)

Sphingosine is not a component of:

glycerophospholipids

Select the fatty acid in each pair that has the higher melting temperature.

16:1c9 or 16:2c9,12
- 16:1c9

18:0 or 18:1c9
- 18:0

18:0 or 20:0
- 20:0

Membranes are generally symmetrical, i.e., the outer face is composed of the same number and types of phospholipids as the inner face.

False

Phospholipids can freely diffuse from the interior leaflet of the plasma membrane to the exterior leaflet without the assistance of enzymes.

False

Triglycerides are fat storage molecules not typically found in membranes.

True

Match the description given with the correct lipid. (Answers may be used more than once)

Primary storage form of lipids.
Triacylglycerols.

Provides stability in the plasma membrane.
Cholesterol

Isoprene derivative
Cholesterol

Commonly found in nervous tissue
Sphingomyelin

Sphingosine backbone with several carbohydrates attached
Ganglioside

Glycerol backbone with two fatty acyl groups
Glycerophospholipid

A membrane's fluidity is largely determined by the percentage of _____________.

unsaturated fats

The concentration of Ca2+ in the endoplasmic reticulum (outside) is 1 mM, and the concentration of Ca2+ in the cytosol (inside) is 0.1 μM. Calculate ΔG at 37°C when the membrane potential is −50 mV (cytosol negative)

-33,388.1

Which of the following is/are true regarding the glucose transporter?

it transports glucose down it's concentration gradient
binding of glucose causes a conformational change so that the transporter is never open on both sides of the membrane

Match the transporter (A- blue, B- green, C- light purple) with it's description.

A - Symporter

B - Uniporter

C - Antiporter

Indicate whether the following compounds are likely to cross a membrane by simple diffusion or facilitated diffusion transport:

aspartic acid
facilitated

carbon dioxide
simple

glucose
facilitated

Which of the following will cause the opening or closing of a gated ion channel?

voltage change

What substance will be transported through an aquaporin?

water

In the sodium-potassium pump:

sodium is transported out of the cell and potassium into the cell, both against concentration gradients

Active transport is uniquely characterized by:

the tight coupling of an input of energy, with the species going from a lesser concentration to a greater concentration.

Facilitated (Mediated) diffusion across a biological membrane:

is driven by a difference in solute concentration.

Energy requiring transport mechanisms include

Active transport

Inside a nerve cell at rest, [Na +] is
____ and [K+] _____ relative to the concentrations seen outside the cell.

low, high

The Hydrophobic Effect

The exclusion of nonpolar substances from an aqueous solution

Amphiphilic

experience both hydrophilic interactions and the hydrophobic effect. most lipids are amphiphilic.

the pH scale

The ionization of water can be described by a dissociation constant, K:

(products)/(reactants)

acid

substance that can donate a proton

base

a substance that can accept a proton

pK helps to

determine the strength of an acid (lower pK = stronger acid, higher pK = weaker acid)

Henderson-Hasselbalch Equation

*pK is the specific pH where there are equal concentrations of base and acid
*log > 1 --> always positive, pH rises
*log < 1 --> always negative, pH lowers

pH < pK

everything will be protonated

buffer

*weak acid/conj base system* aids in resisting changes in the pH of a system

Amino Acids (L and D groups)

L --> amino group to the left of the alpha carbon
D --> amino group to the right of the alpha carbon

L is the most common in nature